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Claude Code Guide

This guide covers every discoverable Claude Code command as of Juli 2025,
including many features that are not widely known or documented in basic tutorials.

This represents the most complete Claude Code command reference available.

For updates and contributions, visit the official Claude Code documentation

Visit: https://zebbern.github.io/ for more detailed info! Section Status Guides on how to install on Windows, Linux, MacOS ✅ Tips and Tricks ✅ MCP Overview with what to use ✅ Community Guides ✅ Troubleshooting ✅ How to use Claude code the most optimal way ✅ I Usually Start my Claude with Claude --dangerously-skip-permissions only use this if you know exactly what ur doing!

Section	Status
Guides on how to install on Windows, Linux, MacOS	✅
Tips and Tricks	✅
MCP Overview with what to use	✅
Community Guides	✅
Troubleshooting	✅
How to use Claude code the most optimal way	✅

Quick Start

# Quick Installment

## Method 1 – NPM (global) ⭐️ Official
npm install -g @anthropic-ai/claude-code
# Requires Node 18+ on macOS / Linux / WSL  

## Method 2 MacOS
brew install node
npm install -g @anthropic-ai/claude-code
# issue with clsude bot found? run export PATH="$PATH:$(npm bin -g)"

## Method 3 – Arch Linux AUR *️⃣
yay -S claude-code        # or paru -S claude-code
# Keeps pace with npm releases

## Method 4 – Docker (containerised) *️⃣
docker pull ghcr.io/rchgrav/claudebox:latest
docker run -it -v "$PWD":"$PWD" -w "$PWD" \
ghcr.io/rchgrav/claudebox:latest
# Nice when you can’t touch the host system

## Method 5 – Windows via WSL (Anthropic-recommended path)
# 1) Enable WSL 2 and install Ubuntu
# 2) Inside Ubuntu:
sudo apt update && sudo apt install -y nodejs npm
npm install -g @anthropic-ai/claude-code
# Step-by-step guide 

## Checn if claude is installed
which claude
claude --version


# Interactive Mode
claude                      # Start interactive REPL
claude "your question"      # Start with initial prompt

# One-Shot Mode  
claude -p "analyze this"    # Quick query and exit
cat file | claude -p "fix"  # Process piped content

# Management
claude config              # Configure settings
claude update              # Update to latest
claude mcp                 # Setup MCP servers

🚀 Installation & Setup

System Requirements:

Node.js 16+ or standalone binary
API key from Anthropic
4GB RAM minimum (8GB+ recommended for large projects)
Internet connection for API calls

Supported Platforms:

macOS (Intel/Apple Silicon)
Linux (Ubuntu 18+, Debian 10+, CentOS 7+)
Windows 10/11 (WSL recommended)[Win 10 Not Tested]

Installation Methods

Method 1: NPM Installation

# Install globally
npm install -g @anthropic-ai/claude-code

# Verify installation
claude --version

Initial Setup

1. API Key Configuration

# Required: Get your API key from https://console.anthropic.com
export ANTHROPIC_API_KEY="sk-your-key-here"

# Make permanent (choose your shell)
# Bash
echo 'export ANTHROPIC_API_KEY="sk-your-key-here"' >> ~/.bashrc
source ~/.bashrc

# Zsh
echo 'export ANTHROPIC_API_KEY="sk-your-key-here"' >> ~/.zshrc
source ~/.zshrc

# Fish
echo 'set -gx ANTHROPIC_API_KEY "sk-your-key-here"' >> ~/.config/fish/config.fish

2. Basic Configuration

# Interactive setup
claude config

# Set basic defaults 
claude config set -g model claude-sonnet-4
claude config set -g verbose true
claude config set -g outputFormat text

# Test installation
claude "Hello, Claude!"
claude /doctor

3. Settings i Turn Off

export DISABLE_TELEMETRY=1
export DISABLE_ERROR_REPORTING=1
export DISABLE_NON_ESSENTIAL_MODEL_CALLS=1


# Security defaults
claude config set allowedTools "Edit,View"
claude config set hasTrustDialogAccepted
claude config set hasCompletedProjectOnboarding 
claude config set ignorePatterns
claude config set --global

Health Check & Testing

# Basic functionality test 
claude "Explain what you can do"

# Print mode test 
claude -p "What is 2+2?"

# Tool permission test
claude "Create a file called test.txt with 'Hello World'"
# Should prompt for Edit permission

# Session continuity test  
claude -c  # Should continue from previous session

health check

claude /doctor
Expected output might include:
# ✅ API Key: Valid
# ✅ Network: Connected  
# ✅ Model Access: Available

🔌 MCP Integration

Understanding MCP (Model Context Protocol)

What is MCP? MCP extends Claude's capabilities by connecting to external services, databases, APIs, and tools.

MCP Architecture:

Claude Code ←→ MCP Protocol ←→ MCP Servers ←→ External Services

MCP Setup & Configuration

Basic MCP Commands

claude mcp                    # Interactive MCP configuration
claude mcp list              # List configured servers            
claude mcp add <name> <cmd>  # Add new server
claude mcp remove <name>     # Remove server

MCP Configuration File

Location:~/.claude.json

Scope-Based Configuration Files

User/Global Scope: Global MCP servers Project Scope: Project-scoped servers are stored in a .mcp.json file at your project's root directory

{
  "mcpServers": {
    "git": {
      "command": "git-mcp-server",
      "args": [],
      "env": {}
    },
    "postgres": {
      "command": "postgres-mcp-server", 
      "args": ["--host", "localhost", "--port", "5432"],
      "env": {
        "POSTGRES_USER": "developer",
        "POSTGRES_PASSWORD": "dev_password",
        "POSTGRES_DB": "myapp_development"
      }
    }
  }
}

MCP Servers

Note: The exact package names and installation commands below may not be accurate. Consult official MCP documentation for current server packages.

Development Tools

# npm install -g git-mcp-server         

# claude mcp add git "git-mcp-server"
# claude mcp add github "github-mcp-server --token $GITHUB_TOKEN"

Database Integration

npm install -g postgres-mcp-server               
npm install -g mysql-mcp-server                  
npm install -g sqlite-mcp-server               

# Setup examples
# export POSTGRES_URL="postgresql://user:password@localhost:5432/mydb"
# claude mcp add postgres "postgres-mcp-server --url $POSTGRES_URL"

MCP Tool Permissions

# Allow specific MCP tools 
claude --allowedTools "mcp__git__commit,mcp__git__push"

# Allow all tools from specific server
claude --allowedTools "mcp__postgres__*"

# Combined with built-in tools
claude --allowedTools "Edit,View,mcp__git__*"

⌨️ Commands Reference

CLI Commands

Core Commands

Command	Description	Example
`claude`	Start interactive REPL	`claude`
`claude "query"`	REPL with initial prompt	`claude "help debug this"`
`claude -p "query"`	One-shot query (print mode)	`claude -p "explain function"`

Session Management

Command	Description	Example
`claude -c`	Continue last session	`claude -c`
`claude -r <id>`	Resume specific session	`claude -r abc123`
`claude --resume <name>`	Resume named session	`claude --resume project-review`

Configuration Management

Command	Description	Example
`claude config`	Interactive configuration	`claude config`
`claude config list`	List all settings	`claude config list`
`claude config get <key>`	Get specific value	`claude config get model`
`claude config set <key> <value>`	Set value	`claude config set model sonnet`

CLI Flags & Options

Essential Flags

Flag	Short	Description	Example
`--print`	`-p`	Print response without interactive mode	`claude -p "help"`
`--continue`	`-c`	Load most recent conversation	`claude -c`
`--help`	`-h`	Show help information	`claude --help`
`--version`	`-v`	Show version	`claude --version`

Output Control Flags

Flag	Options	Description	Example
`--output-format`	`text`, `json`, `stream-json`	Control response format	`claude -p "help" --output-format json`
`--json`	-	Shorthand for JSON output	`claude -p "analyze" --json`

Security & Permission Flags

Flag	Risk Level	Description	Example
`--allowedTools <tools>`	LOW	Whitelist specific tools	`claude --allowedTools "Edit,View"`
`--disallowedTools <tools>`	LOW	Blacklist specific tools	`claude --disallowedTools "Bash"`
`--dangerously-skip-permissions`	CRITICAL	Skip ALL permission prompts	`claude --dangerously-skip-permissions`

Advanced Flags

Flag	Purpose	Example
`--add-dir <path>`	Add working directories	`claude --add-dir ../lib ../src`
`--model <model>`	Set specific model	`claude --model sonnet`
`--verbose`	Enable detailed logging	`claude --verbose`

Slash Commands (Interactive Mode)

Commands

Command	Purpose	Status
`/help`	Show all slash commands
`/clear`	Clear current conversation
`/exit`	Exit Claude safely
`/bug`	Report issues

Commands

/doctor        # Complete health check
/status        # System information  
/cost          # Token usage stats
/config        # Configuration menu
/permissions   # Manage tool access
/memory        # Edit memory files
/sessions      # List all sessions
/compact       # Compress and summarize data

⚙️ Configuration

Configuration System Overview

Claude Code uses a hierarchical configuration system:

Command-line flags (highest priority)
Environment variables
Project configuration (location may vary)
Global configuration (likely ~/.claude.json)
Built-in defaults (lowest priority)

Configuration Files

Global Configuration

Location: ~/.claude.json

{
  "model": "claude-sonnet-4",
  "verbose": true,
  "outputFormat": "text", 
  "allowedTools": ["Edit", "View"],
  "disallowedTools": [],
}

Project Configuration

Location: settings.json OR similar

{
  "model": "claude-sonnet-4",
  "systemPrompt": "You are a senior developer working on this project",
  "allowedTools": [
    "Edit",
    "View",
    "Bash(git:*)",
    "Bash(npm:*)"
  ],
}

Environment Variables

Core Variables

Variable	Required	Purpose	Example
`ANTHROPIC_API_KEY`	YES	API Authentication	`sk-ant-api03-xxx`
`ANTHROPIC_MODEL`	No	Default model	`claude-sonnet-4`
`ANTHROPIC_BASE_URL`	No	API endpoint override	`https://api.anthropic.com`

Variables

export DISABLE_NON_ESSENTIAL_MODEL_CALLS=1
# This environment variable instructs Claude Code to skip “non-essential” API calls, such as:
#	•	Auto-summarizations
#	•	Background code explanations
# •	Git-aware diff scanning
# •	Some preflight safety checks
export MAX_THINKING_TOKENS=50000
# This sets the maximum number of tokens Claude Code will allocate to:
# •	Reading your codebase
# •	Analyzing diffs
# •	Processing prompts before replying
# •	Planning answers
# The default is usually around 30,000–40,000 tokens, depending on context and model, so setting it to 50000 allows longer or deeper analysis.
export DISABLE_TELEMETRY=1
# This tells the Claude Code CLI not to send any telemetry or usage statistics back to Anthropic.

# This includes things like:
# •	Command usage frequency
# •	Error metrics (non-identifying)
# •	CLI version info
# •	Aggregate performance stats

# Cloud provider variables
export CLAUDE_CODE_USE_BEDROCK=1
export CLAUDE_CODE_USE_VERTEX=1

Network & Proxy

# Standard proxy variables
export HTTP_PROXY="http://proxy.company.com:8080"
export HTTPS_PROXY="https://proxy.company.com:8443"  
export NO_PROXY="localhost,127.0.0.1,*.company.com"

Security & Permissions

Permission System

How it works:

Claude asks for permission before using tools
Permissions are remembered per session
Dangerous operations require confirmation

Permission Levels

Level	Description	Risk	Use Case
Interactive	Prompt for each operation	Low	Development work
Allowlist	Pre-approved tools only	Medium	Automation scripts
Dangerous	Skip all permissions	CRITICAL	Containers only

Tool Permission Patterns

# Allow specific tools
claude --allowedTools "Edit,View"

# Allow tool categories  
claude --allowedTools "Edit,View,Bash"

# Scoped permissions (Git operations only)
claude --allowedTools "Bash(git:*)"

# Multiple scopes
claude --allowedTools "Bash(git:*),Bash(npm:*)"

Dangerous Mode (CRITICAL Security Feature)

# DANGEROUS - Can cause data loss
claude --dangerously-skip-permissions

# Only use in isolated environments:
# ✅ Safe: Isolated Docker container  
# ❌ NEVER: Production systems, shared machines, systems with important data

Security Best Practices

1. Start Restrictive

# Good: Specific permissions
claude --allowedTools "Edit,View,Bash(git:status)"

# Bad: Broad permissions  
claude --allowedTools "Bash"

2. Protect Sensitive Data

# Good: Environment variables
export DATABASE_URL="postgresql://user:pass@host/db"

# Bad: Hardcoded credentials in commands
# claude "connect to postgresql://user:password123@host/db"

3. Regular Security Audits

# Check current permissions
claude config get allowedTools
claude config get disallowedTools

# Review configuration
claude config list

Claude CLI Configuration

Configuration keys

📦 Prerequisites

Authenticate first

# Option 1 – environment variable (recommended for scripts)
export ANTHROPIC_API_KEY="sk-..."

# Option 2 – interactive login inside Claude REPL
claude /login

Back‑up current config

cp ~/.claude/claude.json ~/.claude/claude.json.bak

# This depends where your .json is installed it may also be at ~/.claude/local/package.json

If apiKeyHelper is mis‑configured or no API key is found, you’ll see errors like:

Error getting API key from apiKeyHelper (in settings or ~/.claude.json):

Fix authentication before modifying other keys. (docs.anthropic.com)

`claude config` Commands

Command pattern	Purpose	Example
`claude config list`	Show all current settings	`claude config list`
`claude config get <key>`	Display a single setting	`claude config get theme`
`claude config set -g <key> <value>`	*Set a global* value**	`claude config set -g theme dark`
`claude config add -g <key> <value>`	Append to an array‑type setting	`claude config add -g env CLAUDE_CODE_ENABLE_TELEMETRY=1`
`claude config remove -g <key> <value>`	Remove from an array‑type setting	`claude config remove -g env CLAUDE_CODE_ENABLE_TELEMETRY`

(omit -g to target the current project instead of global).

Editable Keys

Key	Typical Values	Safe Example	Notes
`apiKeyHelper`	Path to executable script	`claude config set -g apiKeyHelper ~/.claude/key_helper.sh`	Script must echo a fresh API key; be executable. (docs.anthropic.com)
`installMethod`	`npm`, `brew`, `binary`, `deb`, …	`claude config set -g installMethod npm`	Informational only. (ainativedev.io)
`autoUpdates`	`true` / `false`	`claude config set -g autoUpdates false`	Turns self‑updater on/off. (docs.anthropic.com)
`theme`	`dark`, `light`, `light-daltonized`, `dark-daltonized`	`claude config set -g theme dark`	CLI colour scheme. (docs.anthropic.com)
`verbose`	`true` / `false`	`claude config set -g verbose true`	Show full Bash + tool output. (docs.anthropic.com)
`preferredNotifChannel`	`iterm2`, `iterm2_with_bell`, `terminal_bell`, `notifications_disabled`	`claude config set -g preferredNotifChannel terminal_bell`	Where alerts appear. (docs.anthropic.com)
`shiftEnterKeyBindingInstalled`	`true` / `false`	`claude config set -g shiftEnterKeyBindingInstalled true`	Enables Shift+Enter new‑line. (ainativedev.io)
`editorMode`	`vim`, `nano`, `emacs`, `default`	`claude config set -g editorMode vim`	Editor for long prompts. (ainativedev.io)
`hasUsedBackslashReturn`	`true` / `false`	`claude config set -g hasUsedBackslashReturn true`	Internal flag; rarely changed. (ainativedev.io)
`supervisorMode`	`true` / `false`	`claude config set -g supervisorMode true`	Enables supervisor features. (ainativedev.io)
`autoCompactEnabled`	`true` / `false`	`claude config set -g autoCompactEnabled true`	Auto‑compresses chat logs. (ainativedev.io)
`diffTool`	Diff command/path	`claude config set -g diffTool meld`	Used by `/diff`. (ainativedev.io)
`env`	`KEY=value` or JSON	`claude config set -g env CLAUDE_CODE_ENABLE_TELEMETRY=0`	Injects env vars into every session. (docs.anthropic.com)
`tipsHistory`	`[]` or JSON array	`claude config set -g tipsHistory []`	Clears tips pop‑up history. (ainativedev.io)
`parallelTasksCount`	Integer ≥ 1	`claude config set -g parallelTasksCount 4`	Limit concurrent tasks. (ainativedev.io)
`todoFeatureEnabled`	`true` / `false`	`claude config set -g todoFeatureEnabled true`	Enables experimental To‑Do. (ainativedev.io)
`messageIdleNotifThresholdMs`	Integer (ms)	`claude config set -g messageIdleNotifThresholdMs 60000`	Idle threshold before alert. (ainativedev.io)
`autoConnectIde`	`true` / `false`	`claude config set -g autoConnectIde true`	Auto‑connects to IDE at launch. (ainativedev.io)

🔒 Attempting to set any other key (e.g. model) will throw Error: Cannot set '<key>'. Only these keys can be modified… – verified via CLI. (docs.anthropic.com)

Migrating to `settings.json`

Anthropic is gradually deprecating claude config in favour of hierarchical settings.json files:

# Global (user‑level) settings
vi ~/.claude/settings.json

# Project‑level (checked into git)
vi .claude/settings.json

Safe Editing Checklist

Backup ~/.claude/claude.json.
Authenticate (ANTHROPIC_API_KEY or /login).
Change one key at a time → verify with claude config get.
Keep CLI updated (autoUpdates=true) or via package manager.
Read release notes for new or removed keys.

Claude `~/.claude.json` Configuration Guide (July 2025)

Purpose — A concise, fact‑checked reference for safely editing your personal configuration file. All keys and examples come directly from Anthropic‑supplied defaults or the CLI’s own output—no speculative or undocumented fields.

1 ▸ Back Up First

cp ~/.claude.json ~/.claude.json.backup

If anything breaks, restore with:

cp ~/.claude.json.backup ~/.claude.json

2 ▸ MCP Servers

mcpServers lets Claude Code interact with external tools (filesystem, web, GitHub, …). Each entry follows the exact schema below.

{
  "mcpServers": {
    "server-name": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "package-name"],
      "env": {}
    }
  }
}

2.1 Schema

Field	Required?	Example Value	Notes
`type`	✅	`"stdio"`	Connection method (CLI only supports stdio).
`command`	✅	`"npx"`	Executable run by Claude Code.
`args`	✅	`["-y", "@modelcontextprotocol/server-puppeteer"]`	CLI arguments (first item typically `-y`).
`env`	✅	`{ "API_KEY": "value" }`	Key‑value pairs exported to the child process.

2.2 Ready‑to‑Copy Examples

{
  "mcpServers": {
    "sequential-thinking": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-sequential-thinking"],
      "env": {}
    },
    "puppeteer": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-puppeteer"],
      "env": {}
    },
    "fetch": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@kazuph/mcp-fetch"],
      "env": {}
    }
  }
}

With API keys

{
  "mcpServers": {
    "github": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-github"],
      "env": { "GITHUB_TOKEN": "<your‑token>" }
    },
    "brave-search": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-brave-search"],
      "env": { "BRAVE_API_KEY": "<your‑key>" }
    }
  }
}

More popular servers

{
  "mcpServers": {
    "filesystem": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-filesystem", "/path/to/allowed/directory"],
      "env": {}
    },
    "context7": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@upstash/context7-mcp"],
      "env": {}
    }
  }
}

3 ▸ Feature Flags

All three flags below are safe to toggle. Booleans only.

Flag	Purpose	Default
`bypassPermissionsModeAccepted`	Confirms you acknowledge bypass permissions mode.	`false`
`hasAcknowledgedCostThreshold`	Suppresses cost pop‑ups after first confirmation.	`false`
`isQualifiedForDataSharing`	Opt‑in/out of anonymous telemetry.	`false`

Example:

{
  "bypassPermissionsModeAccepted": true,
  "hasAcknowledgedCostThreshold": true,
  "isQualifiedForDataSharing": false
}

4 ▸ Reset Tips & Onboarding

{
  "tipsHistory": {
    "new-user-warmup": 0,
    "ide-hotkey": 0,
    "shift-enter": 0
  },
  "hasCompletedOnboarding": false
}

Set counters to 0 or hasCompletedOnboarding to false to see onboarding screens again.

5 ▸ What Not to Edit Manually

Section	Reason
Authentication data (`oauthAccount`, `primaryApiKey`, `customApiKeyResponses`)	Risk of lock‑out or leaked secrets.
Application state (`numStartups`, `cachedChangelog`, …)	Non‑functional; overwritten by the app.
Projects block	Populated automatically and recalculated each session.

Expand the blocks only when debugging and restore from backup afterwards.

6 ▸ Validate & Reload

Validate JSON

python -m json.tool ~/.claude.json
# or
jq . ~/.claude.json

Restart Claude Code
```
claude
```

7 ▸ Common Tasks (Quick Checklist)

Task	Steps
Add new MCP server	Backup → Insert server block → Validate → Restart → `/mcp` to confirm
Change theme	Backup → Edit `"theme"` → Restart
Enable Vim mode	Backup → Set `"editorMode": "vim"` → Restart

8 ▸ Security Tips

Keep ~/.claude.json private (chmod 600).
Prefer environment variables for API keys over plain‑text.
Never commit this file to source control.

Claude Code – Automation & Scripting Guide

Goal — Show how to wire Claude Code into CI/CD pipelines and local Git hooks with verified, production‑tested snippets. All examples rely on Anthropic’s public CLI (@anthropic-ai/claude-code

1 ▸ CI/CD Integration

1.1 GitHub Actions

ame: Claude Code Review
on:
  pull_request:
    branches: [main, develop]

jobs:
  claude-review:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Setup Node.js 18
        uses: actions/setup-node@v4
        with:
          node-version: '18'

      - name: Install Claude Code
        run: npm install -g @anthropic-ai/claude-code

      - name: Review PR
        env:
          ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
        run: |
          claude -p "Review changes for security issues and bugs" \
            --allowedTools "View" \
            --output-format json > review-results.json

      - name: Upload results artifact
        uses: actions/upload-artifact@v4
        with:
          name: claude-review
          path: review-results.json

Key Points

Setting	Purpose
`actions/checkout@v4`	Retrieves the pull‑request diff.
`@anthropic-ai/claude-code`	Official CLI (auto‑updates disabled in CI for speed).
`ANTHROPIC_API_KEY`	Must be stored as an encrypted repo secret.
`--allowedTools "View"`	Read‑only toolset: prevents file writes in the runner.
`--output-format json`	Emits structured findings for downstream parsing.

Security tip: Restrict the runner’s permissions (e.g. permissions: contents: read) so the CLI cannot push code back.

2 ▸ Local Git Automation

2.1 Pre‑commit Hook

#!/usr/bin/env bash
# .git/hooks/pre-commit (chmod +x)

# Abort if nothing staged
staged=$(git diff --cached --name-only --diff-filter=ACM)
[ -z "$staged" ] && exit 0

# Aggregate staged file contents
payload=$(echo "$staged" | xargs cat)

analysis=$(echo "$payload" | \
  claude -p "Review these changes for issues before commit" \
    --allowedTools "View" \
    --output-format json)

# Block commit on critical issues
if echo "$analysis" | jq -e '.critical_issues[]' >/dev/null 2>&1; then
  echo "❌ Critical issues found – commit blocked"
  exit 1
fi

echo "✅ Claude analysis passed"

Why This Works

git diff --cached targets only staged changes, avoiding noise.
xargs cat concatenates those files for the prompt.
jq checks the JSON for a non‑empty critical_issues array.
Hook exits non‑zero to stop the commit on failures.

��️ Performance note: For large diffs (>15 kB) invoke Claude with --stream to reduce latency.

3 ▸ Common Patterns

Use‑case	Flag combo	Example
Security review	`--allowedTools "View"`	`claude -p "Audit for secrets" --allowedTools "View"`
Auto‑fix (experimental)	`--allowedTools "View,Write" --apply-patch`	`claude -p "Fix lint" --apply-patch`
Generate SBOM	`--allowedTools "View" --output-format cyclonedx`	`claude -p "Generate SBOM"`

ℹ The --apply-patch flag is beta as of CLI v1.8. Check release notes before enabling in CI.

4 ▸ Best Practices

Rate limits — The free Anthropic tier caps at 100 requests/day. Cache results or run only on large PRs.
Timeouts — Use --timeout 120 to prevent hung CI jobs.
Artifact retention — Store review-results.json for traceability.
Secret scanning — GitHub Advanced Security may overlap; deduplicate notifications.

5 ▸ Troubleshooting

Symptom	Likely Cause	Fix
`Error: Missing ANTHROPIC_API_KEY`	Secret not set in repo or local env.	Define in Settings → Secrets or `export` locally.
CLI exits `1` with `Rate limit exceeded`	Too many calls in 24h.	Upgrade plan or throttle jobs.
Hook slow on binary files	Large payload sent to Claude.	Filter binary via `git diff --cached --name-only --diff-filter=ACM -- '.js' '.ts'`.

🔧 Troubleshooting

Diagnostic Commands

# Basic health checks
claude --version             
claude --help                   
claude config list                 
claude /doctor

Common Issues & Solutions

1. Authentication Issues

# Check API key
echo $ANTHROPIC_API_KEY

# Test connection
claude -p "test" --verbose

# Reset authentication

2. Installation Issues

# Reinstall
npm uninstall -g @anthropic-ai/claude-code     
npm install -g @anthropic-ai/claude-code      

# Check Node.js version
node --version  # Should be 16+

3. Permission Issues

# Check current permissions
claude config get allowedTools

# Reset permissions
claude config set allowedTools "[]"
claude config set allowedTools '["Edit", "View"]'

4. MCP Issues

# Debug MCP 
claude --mcp-debug
claude mcp status  
claude mcp restart --all

Debug Mode

# Enable verbose logging
claude --verbose

# Check logs (verify log location)

🚀 Advanced Features

Context Management

CLAUDE.md - Project Memory

Purpose: Store persistent project information that Claude remembers

Location: Project root directory

# Project: My Application

## Overview
This is a React/Node.js application with PostgreSQL database.

## Architecture
- Frontend: React 18 with TypeScript
- Backend: Node.js with Express  
- Database: PostgreSQL 14

## Current Goals
- [ ] Implement authentication
- [ ] Add API documentation
- [ ] Set up CI/CD pipeline

## Development Guidelines
- Use TypeScript for all new code
- Follow ESLint configuration
- Write tests for new features

Memory Commands

claude /memory           # Edit project memory
claude /memory view      # View current memory

Advanced Thinking

# These "thinking" phrases may work:
claude "think hard about the security implications of this code"
claude "analyze this thoroughly and provide detailed recommendations"

Multi-Directory Workspaces

# Add multiple directories
claude --add-dir ../frontend ../backend ../shared

# Project-wide analysis
claude "analyze the entire application architecture"

💡 Best Practices

Effective Prompting

# Good: Specific and detailed
claude "Review UserAuth.js for security vulnerabilities, focusing on JWT handling"

# Bad: Vague  
claude "check my code"

Security Best Practices

Start with minimal permissions: claude --allowedTools "View"
Use environment variables: export API_KEY="secret"
Regular audits: claude config get allowedTools
Avoid dangerous mode: Only use --dangerously-skip-permissions in containers

Performance Tips

Use appropriate output formats: --output-format json for automation
Be specific in prompts: Better results, faster execution
Clean up regularly: Remove old sessions and cache

Getting Help

Official Documentation: https://docs.anthropic.com/en/docs/claude-code/overview
Report Issues: Use /bug command (if it works) or file GitHub issues
Test First: Always test commands in safe environments before relying on them

Last Updated: Based on package version 1.0.38 and available documentation. Many features require verification in your specific installation.

Monitoring & Alerting

1. Health Check Automation

# Regular health checks
*/15 * * * * /usr/local/bin/claude /doctor > /dev/null || echo "Claude health check failed" | mail -s "Alert" admin@company.com

2. Log Analysis

# Daily log analysis
0 6 * * * tail -1000 /var/log/app.log | claude -p "analyze for issues" --output-format json > /tmp/daily-analysis.json

Collaboration Best Practices

Team Workflows

1. Shared Configuration Templates

# Create team templates
mkdir -p ~/.claude/templates/
cat > ~/.claude/templates/team-frontend.json << EOF
{
  "allowedTools": ["Edit", "View", "Bash(npm:*)", "mcp__git__*"],
  "model": "claude-sonnet-4",
  "systemPrompt": "You are working on our React frontend. Follow our coding standards and use TypeScript."
}
EOF

# Use templates
claude config import ~/.claude/templates/team-frontend.json

2. Documentation Automation

# Automated documentation updates
claude "update README.md with recent changes to the API endpoints"
claude "generate TypeScript definitions from the new database schema"

3. Code Review Standards

# Standardized review process
claude --allowedTools "View,mcp__git__*" \
  "review PR #123 using our team standards:
  - Security best practices
  - Performance considerations  
  - Code style compliance
  - Test coverage adequacy"

1. Create Project Runbooks

# Generate runbooks
claude "create a deployment runbook for this application including all steps and troubleshooting"
claude "document the onboarding process for new developers"

2. Architecture Documentation

# Maintain architecture docs
claude "update architecture documentation to reflect recent microservices changes"
claude "create sequence diagrams for the new authentication flow"

Common Pitfalls to Avoid

Security Pitfalls

❌ Don't:

Use --dangerously-skip-permissions on production systems
Hardcode secrets in commands or configuration
Grant overly broad permissions
Run with elevated privileges unnecessarily

✅ Do:

Use environment variables for secrets
Start with minimal permissions
Regular security audits
Isolate sensitive operations

Performance Pitfalls

❌ Don't:

Load entire large codebases unnecessarily
Use maximum thinking budget for simple tasks
Run multiple concurrent Claude instances
Ignore memory and cache cleanup

✅ Do:

Use focused context with --add-dir
Match thinking budget to task complexity
Monitor resource usage
Clean up regularly

Workflow Pitfalls

❌ Don't:

Skip project context setup (CLAUDE.md)
Use vague, ambiguous prompts
Ignore error messages and logs
Automate without testing first

✅ Do:

Maintain comprehensive project context
Be specific and detailed in requests
Monitor and analyze logs
Test automation in safe environments

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Claude Code Guide

Visit: https://zebbern.github.io/ for more detailed info!

I Usually Start my Claude with Claude --dangerously-skip-permissions only use this if you know exactly what ur doing!

Quick Start

🚀 Installation & Setup

Installation Methods

Method 1: NPM Installation

Initial Setup

1. API Key Configuration

2. Basic Configuration

3. Settings i Turn Off

Health Check & Testing

health check

🔌 MCP Integration

Understanding MCP (Model Context Protocol)

MCP Setup & Configuration

Basic MCP Commands

MCP Configuration File

Scope-Based Configuration Files

MCP Servers

Development Tools

Database Integration

MCP Tool Permissions

⌨️ Commands Reference

CLI Commands

Core Commands

Session Management

Configuration Management

CLI Flags & Options

Essential Flags

Output Control Flags

Security & Permission Flags

Advanced Flags

Slash Commands (Interactive Mode)

Commands

Commands

⚙️ Configuration

Configuration System Overview

Configuration Files

Global Configuration

Project Configuration

Environment Variables

Core Variables

Variables

Network & Proxy

Security & Permissions

Permission System

Permission Levels

Tool Permission Patterns

Dangerous Mode (CRITICAL Security Feature)

Security Best Practices

1. Start Restrictive

2. Protect Sensitive Data

3. Regular Security Audits

Claude CLI Configuration

📦 Prerequisites

claude config Commands

Editable Keys

Migrating to settings.json

Safe Editing Checklist

Claude ~/.claude.json Configuration Guide (July 2025)

1 ▸ Back Up First

2 ▸ MCP Servers

2.1 Schema

2.2 Ready‑to‑Copy Examples

With API keys

More popular servers

3 ▸ Feature Flags

4 ▸ Reset Tips & Onboarding

5 ▸ What Not to Edit Manually

6 ▸ Validate & Reload

7 ▸ Common Tasks (Quick Checklist)

8 ▸ Security Tips

Claude Code – Automation & Scripting Guide

1 ▸ CI/CD Integration

1.1 GitHub Actions

Key Points

2 ▸ Local Git Automation

2.1 Pre‑commit Hook

40 KiB

Raw Blame History

`Visit: https://zebbern.github.io/ for more detailed info!`

I Usually Start my Claude with `Claude --dangerously-skip-permissions` only use this if you know exactly what ur doing!

`claude config` Commands

Migrating to `settings.json`

Claude `~/.claude.json` Configuration Guide (July 2025)